fix: honor deprecated experimental flags instead of ignoring them

[not-matthias]

--experimental-cycle-estimation and --experimental-exclude-allocations were parsed but deliberately dropped. Since --exclude-allocations defaults to false, anyone still passing the old flag silently lost allocation exclusion.

Both now feed their graduated counterparts, and the warning states the truth instead of "has no effect":

⚠ --experimental-exclude-allocations is deprecated and will be removed in a future release: use --exclude-allocations instead.

Closes COD-3511

[greptile-apps]

Confidence Score: 5/5

The PR appears safe to merge, with no outstanding findings in the scoring set.

Summary

This PR restores support for the deprecated cycle-estimation and allocation-exclusion flags by combining them with their graduated counterparts for both run and exec.

• Adds shared resolution helpers for stable and deprecated flags.
• Uses the resolved values when constructing orchestrator configurations.
• Updates deprecation messaging to direct users to the stable flags.

_{Reviews (3) · Last reviewed commit: "fix: honor deprecated experimental flags..."}

[codspeed]

Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 23 untouched benchmarks

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_{Comparing fix/deprecated-experimental-flags (7150303) with main (6c953d6)}